NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
Q86V25 UniProt NPD GO	VASHL_HUMAN	Vasohibin-like protein	0.71	-	nuc	0					355
Q9P0X4 UniProt NPD GO	CAC1I_HUMAN	Voltage-dependent T-type calcium channel subunit alpha-1I (Voltage-gated calcium channel subunit alp ...	0.71	+	end	17	Membrane; multi-pass membrane protein	voltage-gated calcium channel complex [NAS]	608230		2223
Q96LL9 UniProt NPD GO	WBS18_HUMAN	Williams-Beuren syndrome chromosome region 18 protein	0.71	+	nuc	1					226
P50902 UniProt NPD GO	WT1_ALLMI	Wilms' tumor protein (Fragment)	0.71	+	nuc	0	Nucleus				288
Q8C7B8 UniProt NPD GO	ZSWM4_MOUSE	Zinc finger SWIM domain-containing protein 4	0.71	-	nuc	0					1101
P08042 UniProt NPD GO	ZFP1_MOUSE	Zinc finger protein 1 (Zfp-1) (Protein mKR1)	0.71	-	nuc	0	Nucleus (Probable)				402
Q9NR11 UniProt NPD GO	ZN302_HUMAN	Zinc finger protein 302 (ZNF135-like) (ZNF140-like)	0.71	+	nuc	0	Nucleus (Probable)				478
Q5BKZ1 UniProt NPD GO	ZN326_HUMAN	Zinc finger protein 326	0.71	+	nuc	0	Nucleus; nucleoplasm; nuclear matrix (By similarity)				582
Q39264 UniProt NPD GO	ZFP5_ARATH	Zinc finger protein 5	0.71	-	nuc	0					211
O43309 UniProt NPD GO	ZNF96_HUMAN	Zinc finger protein 96 (Zinc finger protein 305) (Zinc finger and SCAN domain-containing protein 12) ...	0.71	-	nuc	0	Nucleus (Potential)		603978		604
O22800 UniProt NPD GO	COL14_ARATH	Zinc finger protein CONSTANS-LIKE 14	0.71	-	nuc	0	Nucleus (Potential)				402
Q7TSX9 UniProt NPD GO	ZAR1_RAT	Zygote arrest 1 (Oocyte-specific maternal effect factor)	0.71	-	nuc	0	Cytoplasm (By similarity)				361
Q61409 UniProt NPD GO	PDE3B_MOUSE	cGMP-inhibited 3',5'-cyclic phosphodiesterase B (EC 3.1.4.17) (Cyclic GMP-inhibited phosphodiesteras ...	0.71	+	nuc	0	Membrane; peripheral membrane protein (Potential)				799
Q28156 UniProt NPD GO	PDE5A_BOVIN	cGMP-specific 3',5'-cyclic phosphodiesterase (EC 3.1.4.35) (CGB-PDE) (cGMP-binding cGMP-specific pho ...	0.71	-	cyt	0				1FL4	865
Q755F7 UniProt NPD GO	CET1_ASHGO	mRNA capping enzyme subunit beta (EC 3.1.3.33) (Polynucleotide 5'-triphosphatase) (mRNA 5'-triphosph ...	0.71	-	nuc	0	Nucleus (By similarity)				478
Q9P6Q6 UniProt NPD GO	CET1_SCHPO	mRNA capping enzyme subunit beta (EC 3.1.3.33) (Polynucleotide 5'-triphosphatase) (mRNA 5'-triphosph ...	0.71	-	nuc	0	Nucleus (By similarity)				303
Q9CYC6 UniProt NPD GO	DCP2_MOUSE	mRNA decapping enzyme 2 (EC 3.-.-.-)	0.71	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Predominantly cytoplasmic, in processing bodies ...				422
Q7RY98 UniProt NPD GO	PALH_NEUCR	pH-response regulator protein palH/rim-21	0.71	-	end	4	Cell membrane; multi-pass membrane protein (By similarity)				778
O93956 UniProt NPD GO	PALI_EMENI	pH-response regulator protein palI/RIM9	0.71	-	nuc	4 *	Cell membrane; multi-pass membrane protein				549
P23796 UniProt NPD GO	RIT1_YEAST	tRNA A64-2'-O-ribosylphosphate transferase (EC 2.4.2.-) (Initiator tRNA phosphoribosyl-transferase)	0.71	-	mit	0		cytoplasm [IDA]			513
P17558 UniProt NPD GO	RTPT_YEAST	40S ribosomal protein PET123, mitochondrial precursor	0.70	-	nuc	0	Mitochondrion	mitochondrial small ribosomal subunit [IDA]			318
P42797 UniProt NPD GO	RT10_ARATH	40S ribosomal protein S10, mitochondrial precursor	0.70	-	mit	0					241
Q56K10 UniProt NPD GO	RS15_BOVIN	40S ribosomal protein S15	0.70	-	nuc	0					144
Q5RDI7 UniProt NPD GO	RS15_PONPY	40S ribosomal protein S15	0.70	-	nuc	0					144
P62846 UniProt NPD GO	RS15_CHICK	40S ribosomal protein S15 (RIG protein)	0.70	-	nuc	0					144
P62841 UniProt NPD GO	RS15_HUMAN	40S ribosomal protein S15 (RIG protein)	0.70	-	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	180535		144
P62842 UniProt NPD GO	RS15_MESAU	40S ribosomal protein S15 (RIG protein)	0.70	-	nuc	0					144
P62843 UniProt NPD GO	RS15_MOUSE	40S ribosomal protein S15 (RIG protein)	0.70	-	nuc	0					144
P62844 UniProt NPD GO	RS15_PIG	40S ribosomal protein S15 (RIG protein)	0.70	-	nuc	0					144
P62845 UniProt NPD GO	RS15_RAT	40S ribosomal protein S15 (RIG protein)	0.70	-	nuc	0					144
Q9FIF3 UniProt NPD GO	RS8_ARATH	40S ribosomal protein S8	0.70	+	nuc	0					210
O81361 UniProt NPD GO	RS8_PRUAR	40S ribosomal protein S8	0.70	+	nuc	0					221
Q62191 UniProt NPD GO	RO52_MOUSE	52 kDa Ro protein (Sjoegren syndrome type A antigen) (SS-A) (Ro(SS-A)) (52 kDa ribonucleoprotein aut ...	0.70	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA]			470
O46157 UniProt NPD GO	RL13_LUMRU	60S ribosomal protein L13	0.70	-	nuc	0					188
P26373 UniProt NPD GO	RL13_HUMAN	60S ribosomal protein L13 (Breast basic conserved protein 1)	0.70	-	nuc	0		cytosolic ribosome (sensu Eukaryota) [TAS]	113703		210
O65055 UniProt NPD GO	RL13A_PICMA	60S ribosomal protein L13a	0.70	-	cyt	0					206
P49693 UniProt NPD GO	RL193_ARATH	60S ribosomal protein L19-3	0.70	-	nuc	0					208
O75969 UniProt NPD GO	AKAP3_HUMAN	A-kinase anchor protein 3 (Protein kinase A-anchoring protein 3) (PRKA3) (A-kinase anchor protein 11 ...	0.70	-	nuc	0	Localizes to the ribs of the fibrous sheath in the principal piece of the sperm tail		604689		853
Q9UIF7 UniProt NPD GO	MUTYH_HUMAN	A/G-specific adenine DNA glycosylase (EC 3.2.2.-) (MutY homolog) (hMYH)	0.70	-	mit	0	Nucleus	nucleus [TAS]	137215	1X51	546
Q4HZ42 UniProt NPD GO	DBP10_GIBZE	ATP-dependent RNA helicase DBP10 (EC 3.6.1.-)	0.70	-	cyt	0	Nucleus; nucleolus (By similarity)				897
Q5A4P9 UniProt NPD GO	DBP9_CANAL	ATP-dependent RNA helicase DBP9 (EC 3.6.1.-)	0.70	-	nuc	0	Nucleus; nucleolus (By similarity)				574
Q03532 UniProt NPD GO	HAS1_YEAST	ATP-dependent RNA helicase HAS1 (EC 3.6.1.-) (Helicase associated with SET1 protein 1)	0.70	+	nuc	0	Nucleus; nucleolus	nuclear envelope [IDA] nucleolus [IDA]			505
Q6CH58 UniProt NPD GO	RRP3_YARLI	ATP-dependent rRNA helicase RRP3 (EC 3.6.1.-)	0.70	+	nuc	0	Nucleus (Probable)				480
Q7RY59 UniProt NPD GO	RRP3_NEUCR	ATP-dependent rRNA helicase rrp-3 (EC 3.6.1.-)	0.70	+	nuc	0	Nucleus (Probable)				515
P33735 UniProt NPD GO	MS2A_DROMA	Accessory gland-specific peptide 26Aa precursor (Male accessory gland secretory protein 355A)	0.70	-	exc	0	Secreted protein; extracellular space				250
Q08641 UniProt NPD GO	AB140_YEAST	Actin-binding protein ABP140	0.70	+	nuc	0	Cytoplasm. Cytoskeleton. Cytoplasmic and cortical cytoskeleton	actin filament [IDA]			627
O02742 UniProt NPD GO	ACK2_BOVIN	Activated CDC42 kinase 2 (EC 2.7.10.2) (ACK-2)	0.70	-	cyt	0					747
Q41274 UniProt NPD GO	AGL8_SINAL	Agamous-like MADS-box protein AGL8 homolog (MADS B)	0.70	-	nuc	0	Nucleus (By similarity)				241
P05094 UniProt NPD GO	ACTN1_CHICK	Alpha-actinin-1 (Alpha-actinin cytoskeletal isoform) (Non-muscle alpha-actinin-1) (F-actin cross lin ...	0.70	-	cyt	0				1SJJ	893
Q9Z1P2 UniProt NPD GO	ACTN1_RAT	Alpha-actinin-1 (Alpha-actinin cytoskeletal isoform) (Non-muscle alpha-actinin-1) (F-actin cross lin ...	0.70	-	nuc	0	Cytoplasm (By similarity). Colocalizes with MYOZ2 and PPP3CA at the Z-line of heart and skeletal mus ...	cytoplasm [IDA] dendritic spine [IDA]			892

You are viewing entries 13601 to 13650 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.